Pretty sure you can, but you would have to locate it - further, I would suggest disabling it rather than deleting it.
Otherwise, take a peek at these:
http://fallout3nexus.com/downloads/file.php?id=11853 (just removes the nearby spawn points, but I would probably suggest running 'Undelete and Disable' in FO3Edit on it just to be safe if they built it poorly)
http://fallout3nexus.com/downloads/file.php?id=12239 (removes the spawn points, puts the Brahmin in a pen, and adds some sandbag placements around the place, would say you probably want to do the same as the other with FO3Edit)